RetrogeneDB ID: retro_etel_1107

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_212792:1536..2044(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000007137
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SFXN3
• Ensembl ID: ENSETEG00000012508
• Aliases: None
• Description: sideroflexin 3 [Source:HGNC Symbol;Acc:16087]

Sequence

>retro_etel_1107
GCCTATGTTTCTGCAACAACGGGTGCTGTAGCAACAGCTCTAGGATTTAACGCACTCACCGAGCATGACTCACCCCTGAT
AGGGCAGTTTGTCCCTTTTGCTGTCGTGGCTGCTGCTAATTGCATTAACATTCCATTAATGAGGCAGAGAGAACTCAAAG
TTGGCATTCCTGTCACTGATGAAAGTGGGAACCGCTGGGGTGAATCAGTGAATGTGAAACAAGCATCGCTCAAGTTGTAG
TCTCCAGAATTCTCATGGCCGCTCCTGGCATGGTGATCCCCCATTCATCATGAACACCTTGGAAAAGAAAGCCTTCTTAA
AGAGGTTCCCCTGGATGAGCGTGCCTATTCAAGTCAGATTGGTTGGCTTCTGTTTGGTGTTTGCTACACCCCTGTGTTGT
GCTCTTTTTCCTCAGTAAAATTCCATGCCTGTGGCAAGTTTGGAGGCTGACCTGCAAGGCAAGATCCAAGAGACCTACCC
TGAGCTGCAGTGCATGTACTTCACCAAG

Alignment

ORF - retro_etel_1107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.9 %
• Parental protein coverage: 52.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AYVSATTGAVATALGLKSLTKHLPPLVGRFVPFAAVAAANCINIPLMR-RELQVGIPVTDEEGQRLGQSV
          AYVSATTGAVATALG...LT.H..PL.G.FVPFA.VAAANCINIPLMR.REL.VGIPVTDE.G.R.G.SV
Retrocopy AYVSATTGAVATALGFNALTEHDSPLIGQFVPFAVVAAANCINIPLMRQRELKVGIPVTDESGNRWGESV

Parental  AAAKQG-IFQVVISRICMAIPAMAIP-PVIMDSLEKKDFLKRRPWLEAPLQMGLVSFCLVFATPLCCALF
          ...KQ..I.QVV.SRI.MA.P.M.IP.P.IM..LEKK.FLKR.PW...P.Q..LV.FCLVFATPLCCALF
Retrocopy NV-KQA<IAQVVVSRILMAAPGMVIP<PFIMNTLEKKAFLKRFPWMSVPIQVRLVGFCLVFATPLCCALF

Parental  PQKSSIRVSRLEPDLRAQIHEQTLSVQVVYYDK
          PQ..S..V..LE.DL...I.E.....Q..Y..K
Retrocopy PQ*NSMPVASLEADLQGKIQETYPELQCMYFTK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1107 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000012508	1 retrocopy	retro_etel_1107 ,
Microcebus murinus	ENSMICG00000000018	2 retrocopies	retro_mmur_1262, retro_mmur_920,